Differential effects of class I isoform histone deacetylase depletion and enzymatic inhibition by belinostat or valproic acid in HeLa cells

Abstract

BackgroundHistone acetylation is an epigenetic modification involved in the regulation of gene expression, balanced by histone acetyl transferases and histone deacetylase (HDAC) enzymes. HDAC inhibitors (HDACi) induce growth arrest and cell death in transformed cells, and are currently in many clinical cancer trials. The transcriptional response to HDACi is complex, as is the response to HDAC isoform knockdown (KD). Here, we describe for the first time in a human cancer cell line, a transcriptional comparison of treatment by two structurally unrelated HDACi; belinostat and valproic acid with the KD of HDAC1, 2 and 3 isoforms.ResultsHDAC KD showed anti-proliferative effects, although to a lesser extent than HDACi treatment. Moreover, we found a 2-fold increased resistance of HDAC1 knockdown cells to belinostat, suggesting this isoenzyme as a selective target. While both HDACi treatment and individual class I HDAC KD produce significant transcriptional effects, three-times higher for HDACi, the gene-expression profiles of class I HDAC KD compared with that obtained by HDACi treatment exhibited less than 4% of altered genes in common between the two modes of inhibition. Further, cell-specific effects of HDAC KD are evident by comparison with a recent study in a different cell line.ConclusionThe increased resistance to belinostat in response to HDAC1 depletion indicates the possibility of using this isoform as a predictive biomarker of response to HDACi treatment. Further, the transcriptional response to chemical inhibition of HDACs is very different from that of KD of individual class I HDAC isoforms. These data suggest that the anti-tumor effect of HDACi is indeed linked to class I inhibition, but may be more complex than simply targeting individual HDAC enzymes.

Chromatin-targeting small molecules cause class-specific transcriptional changes in pancreatic endocrine cells

“…Although we cannot be certain that the down-regulated transcripts we observe are direct targets of HDAC-mediated activation, the appearance of geneexpression changes within 6 h after HDAC inhibitor treatment, and the low number of changes at 1 h after treatment, are consistent with locus-specific repressive roles of histone acetylation. These results correlate with previous findings, including activating roles for HDACs in yeast (32) and mammalian cells (33), and extend these data by excluding compensatory effects following genetic manipulations and prolonged compound treatment.…”

“…Expression studies of compounds inhibiting chromatin-modifying enzymes have focused on HDAC inhibitors in cancer cells (33,(40)(41)(42)(43), including the approved drugs vorinostat and romidepsin. Whereas compounds showing selectivity for single proteins out of the 11 human class I and class II HDAC homologs have remained elusive, the currently available compounds show wide chemical variability.…”

The Histone Deacetylase Inhibitor MGCD0103 Has Both Deacetylase and Microtubule Inhibitory Activity

“…The absence of a G 1 arrest accounts for the higher proportion of an MGCD0103-treated, asynchronously growing population to enter mitosis, whereas other HDACis that induce rapid p21 (Saito et al, 1999), indicating that the effect of MGCD0103 may be related to the spectrum of HDAC inhibited by the drug rather than a normal consequence of generally inhibiting class I HDAC. SiRNA depletion of individual class I HDACs has less effect on gene expression than pan-isoform HDACi, but the effects also seem to be cell line-specific (Senese et al, 2007;Dejligbjerg et al, 2008). HDAC3 has been shown to be directly involved in mitosis.…”

N-(2-hydroxyphenyl)-2-propylpentanamide, a valproic acid aryl derivative designed in silico with improved anti-proliferative activity in HeLa, rhabdomyosarcoma and breast cancer cells

“…With the curve, it was possible to calculate the IC 50 on HeLa cells for each compound, resulting in 0.92 mM for 2 and 9.12 mM for VPA. The IC 50 value for VPA was calculated as previously reported using a concentration 3 mM 42 . Once obtaining the IC 50 for each drug, we seeded 1 Â 10 6 cells in 25 mL culture flasks, each with 5 mL of DMEM medium (alone or in combination with the IC 50 of one of the drugs).…”